Question: Is Xenium compatible with tissues stained with fluorescent dyes?
Answer: Fluorescent dyes are chemical compounds that emit light in visible wavelengths are likely not compatible with Xenium. Some examples of dyes include Alexa Fluor 488 and Evans Blue. While we have not specifically tested these dyes in-house, dyes (fluorescent or otherwise) may impact rolling circle product detection on the Xenium Analyzer. Furthermore, our proprietary autofluorescence quencher may not effectively quench fluorescent dyes in general and we do not recommend alternative quenching methods with Xenium, so additional sources of fluorescence can be a concern.
For FFPE samples, if a specific dye is removed during the deparaffinization process, by visible inspection, it may be lower risk. This said, we haven’t tested tissues stained with dye for Xenium and are unable to determine the potential impacts on assay performance. If considering running samples with dyes on Xenium, not recommended, a small pilot experiment is optimal.
The information provided here may not be applicable to fluorescent proteins or biological pigment molecules. Xenium may be compatible with tissues expressing fluorescent proteins as these molecules are different in composition than chemical dyes.
Product: Xenium In Situ Gene Expression